# HG changeset patch
# User peterjc
# Date 1398856917 14400
# Node ID e59904c855ae3a1e508a406df55035817f2eec49
# Parent a2fb1e67bd113c173c42560ef88f988dd508464e
Uploaded v0.0.10, adds a test and updated download URL
diff -r a2fb1e67bd11 -r e59904c855ae test-data/empty_file.dat
diff -r a2fb1e67bd11 -r e59904c855ae tools/mira3/README.rst
--- a/tools/mira3/README.rst Thu Jan 30 13:21:21 2014 -0500
+++ b/tools/mira3/README.rst Wed Apr 30 07:21:57 2014 -0400
@@ -17,7 +17,7 @@
======================
This should be straightforward, Galaxy should automatically download and
-install the precompiled binary for MIRA v3.4.0 for the Galaxy wrapper,
+install the precompiled binary for MIRA v3.4.1.1 for the Galaxy wrapper,
and run any tests.
@@ -26,12 +26,12 @@
There are just two Galaxy files to install:
-* mira.py (the Python script)
-* mira.xml (the Galaxy tool definition)
+* ``mira.py`` (the Python script)
+* ``mira.xml`` (the Galaxy tool definition)
-The suggested location is a new tools/mira3 folder. You will also need to
-modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do
-this to tools_conf.xml.sample in order to run any tests::
+The suggested location is a new ``tools/mira3`` folder. You will also need to
+modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool, and also do
+this to ``tools_conf.xml.sample`` in order to run any tests::
@@ -74,7 +74,9 @@
- Updated citation information (Cock et al. 2013).
- Development moved to GitHub, https://github.com/peterjc/pico_galaxy
v0.0.9 - Renamed folder mira_assembler to mira3 (see also MIRA 4 wrapper).
- - Correct path issue in automated dependency installation
+ - Correct path issue in automated dependency installation.
+v0.0.10 - Added a functional test.
+ - Updated URL for automated installation of MIRA v3.4.1.1
======= ======================================================================
@@ -90,7 +92,7 @@
For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
the following command from the Galaxy root folder::
- $ tar -czf mira3_wrapper.tar.gz tools/mira3/README.rst tools/mira3/mira.xml tools/mira3/mira.py tools/mira3/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta
+ $ tar -czf mira3_wrapper.tar.gz tools/mira3/README.rst tools/mira3/mira.xml tools/mira3/mira.py tools/mira3/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/empty_file.dat
Check this worked::
@@ -101,6 +103,7 @@
tools/mira3/tool_dependencies.xml
test-data/tvc_mini.fastq
test-data/tvc_contigs.fasta
+ test-data/empty_file.dat
Licence (MIT)
diff -r a2fb1e67bd11 -r e59904c855ae tools/mira3/mira.xml
--- a/tools/mira3/mira.xml Thu Jan 30 13:21:21 2014 -0500
+++ b/tools/mira3/mira.xml Wed Apr 30 07:21:57 2014 -0400
@@ -1,4 +1,4 @@
-
+Takes Sanger, Roche, Illumina, and Ion Torrent datamira
@@ -72,61 +72,61 @@
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
@@ -138,24 +138,25 @@
-
-
-
-
-
-
-
-
+
+
+
+
+
+
-
--->
+
+
+
+
+
+
diff -r a2fb1e67bd11 -r e59904c855ae tools/mira3/tool_dependencies.xml
--- a/tools/mira3/tool_dependencies.xml Thu Jan 30 13:21:21 2014 -0500
+++ b/tools/mira3/tool_dependencies.xml Wed Apr 30 07:21:57 2014 -0400
@@ -4,7 +4,7 @@
- http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_3.4.1.1_prod_linux-gnu_x86_64_static.tar.bz2
+ http://downloads.sourceforge.net/project/mira-assembler/MIRA/Older%20releases/V3.4.0/mira_3.4.1.1_prod_linux-gnu_x86_64_static.tar.bz2bin$INSTALL_DIR